normalized spectral abundance factor done

src/core/proteinmatch.cpp

@@ -326,11 +326,17 @@ pappso::pappso_double ProteinMatch::getLogEvalue(const MsRun * sp_msrun_id) cons
 
 }
 pappso::pappso_double  ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum, const MsRun * p_msrun_id) const {
+    if (proto_nsaf_sum == 0) {
+        throw pappso::PappsoException(QObject::tr("Error computing NSAF for protein %1 :\nproto_nsaf_sum is null").arg(this->getProteinXtpSp().get()->getAccession()));
+    }
     return (getProtoNsaf(p_msrun_id)/proto_nsaf_sum);
 }
 
 pappso::pappso_double ProteinMatch::getProtoNsaf(const MsRun * sp_msrun_id) const {
     try {
+        if (_protein_sp.get()->size() < 1) {
+        throw pappso::PappsoException(QObject::tr("protein has no amino acid sequence"));
+    }
         pappso::pappso_double proto_nsaf =  (pappso::pappso_double) countSampleScan(ValidationState::validAndChecked ,sp_msrun_id) / (pappso::pappso_double) _protein_sp.get()->size();
         return proto_nsaf;
 

src/core/proteinmatch.h

@@ -45,7 +45,7 @@ public:
     ~ProteinMatch();
 
     const ProteinXtpSp & getProteinXtpSp() const;
-    
+
     /** @brief compute protein log10(Evalue) within samples
       * */
     pappso::pappso_double getLogEvalue(const MsRun * sp_msrun_id = nullptr) const;
@@ -64,17 +64,18 @@ public:
      **/
     const QString getHtmlSequence(PeptideEvidence * peptide_evidence_to_locate = nullptr) const;
 
-        /** @brief compute proto NSAF within msrun
-     * Warning: this is not NSAF, just a part
-     * @param p_msrun_id pointer on the msrun to get NSAF.
-     * */
+    /** @brief compute proto NSAF within msrun : spectral abundance factor (SAF)
+    * Warning: this is not NSAF, just a part
+    * @param p_msrun_id pointer on the msrun to get NSAF.
+    * */
     pappso::pappso_double getProtoNsaf(const MsRun * p_msrun_id) const;
 
-            /** @brief compute NSAF within msrun
-     * Warning: this is not NSAF, just a part
-     * @param proto_nsaf_sum the sum of proto nsaf of all proteins within the msrun
-     * @param p_msrun_id pointer on the msrun to get NSAF
-     * */
+    /** @brief compute NSAF within msrun : normalized spectral abundance factor (NSAF)
+     * Florens L., Carozza M. J. C., Swanson S. K., et al. Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods. 2006;40(4):303–311. doi: 10.1016/j.ymeth.2006.07.028.
+    * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1815300/
+    * @param proto_nsaf_sum the sum of SAF of all proteins within the msrun
+    * @param p_msrun_id pointer on the msrun to get NSAF
+    * */
     pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum, const MsRun * p_msrun_id) const;
 
     /** @brief compute Protein Abundance Index (PAI) within sample
@@ -91,7 +92,7 @@ public:
     void addPeptideMatch(const PeptideMatch & peptide_match);
     std::vector<PeptideMatch> & getPeptideMatchList();
     const std::vector<PeptideMatch> & getPeptideMatchList() const;
-    
+
     /** @brief get peptide match sublist with required validation state
      * @param state the validation state to select
      * @param sp_msrun_id the msrun to look for, if nullptr, then get peptide match overall MSruns
@@ -106,15 +107,15 @@ public:
     bool isGrouped() const;
 
     ValidationState getValidationState() const;
-    
+
     /** @brief count peptide match (psm) listed in this protein match
      */
     unsigned int countPeptideMatch(ValidationState state) const;
-    
+
     /** @brief count distinct sample + scans implied in this protein identification
      */
     unsigned int countSampleScan(ValidationState state, const MsRun * p_msrun_id=nullptr) const;
-    
+
     /** @brief count peptide (peptide+mass)
      */
     void countPeptideMass(std::vector<pappso::GrpPeptide *> & count_peptide_mass, ValidationState state) const;
@@ -130,17 +131,17 @@ public:
     * */
     void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
 
-    
+
     /** @brief collect distinct peptide evidences
      */
     void collectPeptideEvidences(std::set<const PeptideEvidence *> & peptide_evidence_set, ValidationState state) const;
-    
+
     /** @brief count distinct sequence taking into account equivalence between Leucine and Isoleucine
      * @param state validation state of peptides to count
      * @param p_msrun_id count within the specified sample
      */
     size_t countSequenceLi(ValidationState state,const MsRun * p_msrun_id=nullptr) const;
-    
+
     /** @brief count distinct peptide+mass+charge
      * peptide is the peptide sequence LI (Leucine => Isoleucine)
      * mass is the peptide mass, not considering labelled residues (if any)
@@ -148,7 +149,7 @@ public:
      * @param p_msrun_id count within the specified sample
      */
     unsigned int countPeptideMassCharge(ValidationState state, const MsRun * sp_msrun_id=nullptr) const;
-   
+
     /** @brief count distinct MS samples in which the protein is observed
      * @param state validation state of peptides to count
      */

src/gui/export_spreadsheet_dialog/export_spreadsheet_dialog.ui

@@ -64,6 +64,9 @@
       </item>
       <item>
        <widget class="QGroupBox" name="compar_groupbox">
+        <property name="toolTip">
+         <string/>
+        </property>
         <property name="title">
          <string>Compar</string>
         </property>
@@ -110,6 +113,16 @@
            </property>
           </widget>
          </item>
+         <item row="0" column="3">
+          <widget class="QCheckBox" name="comparnsaf_checkbox">
+           <property name="toolTip">
+            <string>normalized spectral abundance factor (NSAF)</string>
+           </property>
+           <property name="text">
+            <string>NSAF</string>
+           </property>
+          </widget>
+         </item>
         </layout>
        </widget>
       </item>
@@ -328,7 +341,7 @@
    <slot>doComparUniqueSequence(bool)</slot>
    <hints>
     <hint type="sourcelabel">
-     <x>437</x>
+     <x>359</x>
      <y>296</y>
     </hint>
     <hint type="destinationlabel">
@@ -344,7 +357,7 @@
    <slot>doComparSpecificSpectra(bool)</slot>
    <hints>
     <hint type="sourcelabel">
-     <x>231</x>
+     <x>167</x>
      <y>328</y>
     </hint>
     <hint type="destinationlabel">
@@ -360,7 +373,7 @@
    <slot>doComparSpecificUniqueSequence(bool)</slot>
    <hints>
     <hint type="sourcelabel">
-     <x>437</x>
+     <x>359</x>
      <y>328</y>
     </hint>
     <hint type="destinationlabel">
@@ -376,7 +389,7 @@
    <slot>doComparPai(bool)</slot>
    <hints>
     <hint type="sourcelabel">
-     <x>642</x>
+     <x>501</x>
      <y>296</y>
     </hint>
     <hint type="destinationlabel">
@@ -392,7 +405,7 @@
    <slot>doComparEmpai(bool)</slot>
    <hints>
     <hint type="sourcelabel">
-     <x>642</x>
+     <x>501</x>
      <y>328</y>
     </hint>
     <hint type="destinationlabel">
@@ -433,6 +446,22 @@
     </hint>
    </hints>
   </connection>
+  <connection>
+   <sender>comparnsaf_checkbox</sender>
+   <signal>toggled(bool)</signal>
+   <receiver>ExportSpreadsheetDialog</receiver>
+   <slot>doComparNsaf(bool)</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>550</x>
+     <y>286</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>806</x>
+     <y>294</y>
+    </hint>
+   </hints>
+  </connection>
  </connections>
  <slots>
   <slot>reject()</slot>
@@ -452,5 +481,6 @@
   <slot>doComparEmpai(bool)</slot>
   <slot>doPtmIslands(bool)</slot>
   <slot>doPtmSpectra(bool)</slot>
+  <slot>doComparNsaf(bool)</slot>
  </slots>
 </ui>

src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp

@@ -88,6 +88,10 @@ ExportSpreadsheetDialog::ExportSpreadsheetDialog(QWidget * parent):
     if (settings.value("export_ods/comparempai", "true").toBool()) {
         ui->comparempai_checkbox->setCheckState(Qt::Checked);
     }
+    ui->comparnsaf_checkbox->setCheckState(Qt::Unchecked);
+    if (settings.value("export_ods/comparnsaf", "true").toBool()) {
+        ui->comparnsaf_checkbox->setCheckState(Qt::Checked);
+    }
     ui->samples_checkbox->setCheckState(Qt::Unchecked);
     if (settings.value("export_ods/samples", "true").toBool()) {
         ui->samples_checkbox->setCheckState(Qt::Checked);
@@ -170,6 +174,11 @@ void ExportSpreadsheetDialog::doComparPai(bool simple) {
     QSettings settings;
     settings.setValue("export_ods/comparpai", QString("%1").arg(simple));
 }
+void ExportSpreadsheetDialog::doComparNsaf(bool simple) {
+
+    QSettings settings;
+    settings.setValue("export_ods/comparnsaf", QString("%1").arg(simple));
+}
 void ExportSpreadsheetDialog::doPeptidePos(bool simple) {
 
     QSettings settings;

src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.h

@@ -50,6 +50,7 @@ public slots:
     void doGroups(bool simple);
     void doPeptidePos(bool simple);
     void doComparEmpai(bool simple);
+    void doComparNsaf(bool simple);
     void doComparPai(bool simple);
     void doComparSpecificUniqueSequence(bool simple);
     void doComparUniqueSequence(bool simple);

src/input/xtpxpipsaxhandler.cpp

@@ -493,18 +493,28 @@ bool XtpXpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
         </protein>
               */
     _sp_current_protein = ProteinXtp().makeProteinXtpSp();
-
-    _sp_current_protein.get()->setFastaFileP(_map_fasta_files.at(attributes.value("fasta_id")).get());
+    
+    auto fasta_it = _map_fasta_files.find(attributes.value("fasta_id"));
+    if (fasta_it == _map_fasta_files.end()) {
+        throw pappso::ExceptionNotFound(QObject::tr("ERROR fasta_id %1 not found").arg(attributes.value("fasta_id")));
+    }
+     //qDebug() << "startElement_protein fastaid=" << attributes.value("fasta_id");
+    _sp_current_protein.get()->setFastaFileP(fasta_it->second.get());
     _sp_current_protein.get()->setAccession(attributes.value("acc"));
+    
+     //qDebug() << "startElement_protein acc=" << attributes.value("acc");
+     //qDebug() << "startElement_protein description=" << attributes.value("description");
     _sp_current_protein.get()->setDescription(attributes.value("description"));
     _sp_current_protein.get()->setIsContaminant(false);
     if (attributes.value("is_contaminant").simplified().toLower() == "true") {
         _sp_current_protein.get()->setIsContaminant(true);
     }
+    //qDebug() << "startElement_protein iscontaminant";
     _sp_current_protein.get()->setIsDecoy(false);
     if (attributes.value("is_decoy").simplified().toLower() == "true") {
         _sp_current_protein.get()->setIsDecoy(true);
     }
+    //qDebug() << "startElement_protein isdecoy";
 
     qDebug() << "startElement_protein end" ;
     return true;

src/output/ods/comparbasesheet.cpp

@@ -129,6 +129,7 @@ void ComparBaseSheet::writeProteinMatch(const ProteinMatch * p_protein_match) {
 
 void ComparBaseSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
     qDebug() << "ComparBaseSheet::writeIdentificationGroup begin";
+    _p_current_identification_group = p_ident;
     writeHeaders(p_ident);
 
 

src/output/ods/comparbasesheet.h

@@ -42,12 +42,12 @@ public :
 private :
     void writeIdentificationGroup(IdentificationGroup * p_ident);
     void writeHeaders(IdentificationGroup * p_ident);
-    void writeProteinMatch(const ProteinMatch * p_protein_match);
-
 public :
     void writeSheet();
 protected :
     virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun)=0;
+    void writeProteinMatch(const ProteinMatch * p_protein_match);
+
 
 protected :
     OdsExport * _p_ods_export;
@@ -58,6 +58,8 @@ protected :
     
     QString _first_cell_coordinate;
     
+    IdentificationGroup * _p_current_identification_group;
+    
 };
 
 #endif // COMPARBASESHEET_H

src/output/ods/comparspectrasheet.cpp

@@ -74,3 +74,24 @@ void ComparEmpaiSheet::writeComparValue(const ProteinMatch * p_protein_match, Va
     _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun));
     qDebug() << "ComparEmpaiSheet::writeComparValue end";
 }
+
+ComparNsafSheet::ComparNsafSheet(OdsExport* p_ods_export, CalcWriterInterface* p_writer, const Project* p_project): ComparBaseSheet(p_ods_export, p_writer, p_project) {
+    _title_sheet =  "compar NSAF";
+}
+
+void ComparNsafSheet::writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) {
+    qDebug() << "ComparNsafSheet::writeComparValue begin";
+    pappso::pappso_double proto_nsaf_sum=0;
+    std::pair<std::map<const MsRun *,pappso::pappso_double>::iterator,bool> ret = _map_proto_nsaf_sum_by_msrun.insert(std::pair<const MsRun *,pappso::pappso_double>(p_msrun,0));
+  if (ret.second==false) {
+    //"element 'z' already existed";
+    proto_nsaf_sum = ret.first->second;
+  }
+  else {
+      proto_nsaf_sum = _p_current_identification_group->computeProtoNsafSum(p_msrun);
+      ret.first->second = proto_nsaf_sum;
+  }
+
+    _p_writer->writeCell(p_protein_match->getNsaf(proto_nsaf_sum,p_msrun));
+    qDebug() << "ComparNsafSheet::writeComparValue end";
+}

src/output/ods/comparspectrasheet.h

@@ -69,4 +69,16 @@ protected :
     virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) override;
 };
 
+class ComparNsafSheet:public ComparBaseSheet
+{
+public :
+    ComparNsafSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project);
+
+protected :
+    virtual void writeComparValue(const ProteinMatch * p_protein_match, ValidationState state, const MsRun * p_msrun) override;
+private:
+    
+    std::map<const MsRun *, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;
+};
+
 #endif // COMPARSPECTRASHEET_H

src/output/ods/odsexport.cpp

@@ -114,6 +114,10 @@ void OdsExport::write(CalcWriterInterface * p_writer, WorkMonitorInterface * p_m
             p_monitor->message(QObject::tr("writing emPAI comparisons"));
             ComparEmpaiSheet(this, p_writer, _p_project).writeSheet();
         }
+        if (settings.value("export_ods/comparnsaf", "true").toBool()) {
+            p_monitor->message(QObject::tr("writing NSAF comparisons"));
+            ComparNsafSheet(this, p_writer, _p_project).writeSheet();
+        }
     }
     if (settings.value("export_ods/samples", "true").toBool()) {
         p_monitor->message(QObject::tr("writing samples"));